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Metavirome-assembled genome sequence of a new aquatic RNA virus expands the genus Locarnavirus

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Abstract

RNA viruses in marine environments have long been recognized as major players in the virosphere. In this study, the complete genome sequence of an RNA virus from Yangshan Harbor, named marine RNA virus Yangshan-LWW (YS-LWW), was obtained based on metavirome assembly. The genome of YS-LWW is 8839 nt in length and contains two open reading frames (ORFs). Both RdRP- and whole-genome-based phylogenetic analysis showed that YS-LWW, together with 45 viral isolates with sequences in public datasets, represents a new species in the genus Locarnavirus of the family Marnaviridae. PCR and public dataset mining indicate that YS-LWW and YS-LWW-like viruses have been widely detected in coastal and freshwater environments, suggesting that they might play a significant role in aquatic ecosystems.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (32370151, 41376135).

Author information

Authors and Affiliations

  1. College of Food Science and Technology, Shanghai Ocean University, Shanghai, China

    Fangxin Lu, Shuang Wu, Yimin Ni, Yongxin Yu & Yongjie Wang

  2. Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian Ocean University, Dalian, China

    Songzhe Fu

  3. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China

    Yongjie Wang

  4. Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China

    Yongjie Wang

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Fangxin Lu and Shuang Wu contributed equally to this work.

Electronic Supplementary Material

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Supplementary Data S1 The complete genome of YS-LWW.

Supplementary Data S2 The complete RdRP sequences of the 126 viruses analyzed.

Supplementary Data S3 The RdRP palm domain sequences of the 126 viruses analyzed.

705_2023_5908_MOESM4_ESM.jpg

Supplementary Fig. S1 Maximum-likelihood tree constructed using the RdRP palm domain region of the 126 viral sequences. The inner ring shows the taxonomic rank, and the outer ring shows the sources of the viral genomic sequences. Forty-five taxonomically undetermined viruses are indicated by stars. Bootstrap support values were calculated by 1000 iterations of tree reorganization implemented in FastTree.

705_2023_5908_MOESM5_ESM.jpg

Supplementary Fig. S2 Heat map of the pairwise proteomic similarities of the 92 viruses clustered in the proposed locarna-like clade.

Supplementary Fig. S3 Heat map of the pairwise proteomic similarities of the 126 viruses.

Supplementary Table S1 The coordinates of the sampling sites.

705_2023_5908_MOESM8_ESM.xls

Supplementary Table S2 The estimated genome completeness of the 126 viruses analyzed and their taxonomic information in NCBI

Supplementary Table S3 The YS-LWW-like sequences discovered in the public datasets.

705_2023_5908_MOESM10_ESM.xls

Supplementary Table S4 Sequence similarities of the YS-LWW RdRPs detected in different samples by using the nested RT-PCR.

705_2023_5908_MOESM11_ESM.xls

Supplementary Table S5 Sources of the 126 viral sequences analyzed in this study. The 92 viruses clustered in the proposed locarna-like clade, and the 45 suggested novel members of the genus Locarnavirus are shown in the separated sheets.

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Lu, F., Wu, S., Ni, Y. et al. Metavirome-assembled genome sequence of a new aquatic RNA virus expands the genus Locarnavirus. Arch Virol 168, 279 (2023). https://doi.org/10.1007/s00705-023-05908-1

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